ctDNA Panel Research Articles

Clinical utility of circulating tumor DNA sequencing with a large panel in patients with advanced soft-tissue sarcomas.

11550 Background: Preliminary studies have suggested that the detection, quantification, and profiling of ctDNA in patients with sarcoma is feasible and may improve prognostication, measure treatment response, and detect relapse. However, data related to impact of ctDNA profiling to tailor therapy in patients with advanced disease are lacking. Methods: Patients with advanced soft-tissue sarcomas (STS) have been included in two ongoing institutional molecular profiling studies (BIP: NCT02534649, STING: NCT04932525). Genomic analysis (ctDNA in all cases and tissue when available) was performed by using the Foundation One Liquid CDx Assay (324 genes, tumor mutational burden [TMB], microsatellite instability status). Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumour board dedicated to precision medicine, attended by experts in clinical oncology, molecular biology, and clinical genetics. Actionable targets were defined by the MTB according to the existing level of evidence (ESCAT), and molecular-based treatment suggestions were proposed where possible. Results: Between December 2020 and August 2021, 98 patients with metastatic STS underwent ctDNA profiling. Median time to assay results was 12 days. Results were contributive for 86 patients (88%). At least one actionable target (range 1-4) was detected in 35 patients (36%) including high tumor mutational burden (> 16 mutations/Mb) for 1 patient (1%) and alteration of the DNA repair response pathway for 12 patients (12%). Overall, the MTB recommended a matched therapy for 27 patients (28%). 40 patients underwent also NGS of tissue besides ctDNA profiling. The number of actionable alterations was similar in 26 (65%), whereas it was higher in tissue for 10 (25%) and in liquid for 4 (10%) patients. Conclusions: This large-scale study demonstrates that liquid biopsy with a large NGS ctDNA panel is an efficient approach to match patients to genomically directed clinical trials/targeted therapies in patients with advanced STS. Outcomes of patients treated with matched therapy will be presented at the meeting.

Leveraging personalized circulating tumor DNA (ctDNA) for detection and monitoring of molecular residual disease in high-risk melanoma.

9579 Background: High-risk melanoma has variable prognosis. Adjuvant immuno- (IO) and targeted therapy (TT) are approved for stage III-IV resected disease. However, a significant proportion of patients (pts) are cured by local treatment alone or relapse despite adjuvant therapy. Liquid biopsy with ctDNA assays have been used to predict response to treatment and identify pts at higher risk of progression/death. Personalized ctDNA assays are a highly sensitive approach that may enhance upfront risk stratification and early detection of relapse. Methods: Serial ctDNA Monitoring as a predictive Biomarker in advanced neoplAsms (SAMBA) is a Princess Margaret prospective ctDNA kinetics study (NCT03702309) in high-risk melanoma pts. Plasma is collected pre-op (pre-local treatment, if feasible), post-op (after surgery), and every 3-6 months (m) until radiological progressive disease (rPD). Personalized amplicon based NGS assays by Inivata (RaDaR) were used to detect somatic variants in ctDNA identified through whole-exome sequencing of matched tumor tissue. Progression free survival (PFS) and overall survival (OS) from the time of surgery were estimated with the Kaplan Meier and compared with the log-rank test. Results: As of December 2021, 82 of 100 planned pts have been enrolled. A total of 191 samples from 47 pts have been analyzed. Median age was 66 years (27-87), 33 were male (70%). Seven (15%), 30 (64%) and 10 (21%) were stage II/III/IV respectively. All pts had surgery and 8 (17%) adjuvant radiation. No systemic therapy was given to 11 pts (23%); 30 (64%) had IO and 6 (13%) TT. rPD occurred in 13 pts (28%). Median follow up was 24 months. A median of 48 variants were included in the personalized ctDNA panel design (35-52). ctDNA was detected (ctDNA+) at any time point in 12/47 pts (26%), of which 5/12 (42%) were BRAF and NRAS wt on tissue. Median PFS was 4.9 months (m) for ctDNA+ pts and not reached (NR) for ctDNA- pts at post-op (HR = 2.71 CI 0.60-12.31, p = 0.179). Median OS was 23.1 m vs NR in ctDNA+ vs ctDNA- pts (HR = 8.9, CI 1.45-54.77, p = 0.004). Two ctDNA+ pts had neoadjuvant IO and became ctDNA- before surgery. One, free of disease after 12 m, had ctDNA- in 4 follow up samples. The other pt was ctDNA+ in the post-op sample and relapsed within 3 m. Four of 45 (9%) pts had ctDNA+ at post-op. Two of them, including a pt who had neoadjuvant IO, did not receive adjuvant therapy and had rPD within 3 m. The other 2 pts received adjuvant IO; ctDNA cleared and pts remain free of disease at 12 and 34 m. Three pts with rising ctDNA over time experienced rPD after a median of 4 m (2-7). Conclusions: Personalized ctDNA analysis with RaDaR may improve risk of death stratification and selection of pts who could benefit from adjuvant treatment. Detection of ctDNA may precede rPD. Follow-up will continue in pts with rising ctDNA who have not yet had rPD. Pts accrual and sample collection are ongoing, and additional data will be presented. Clinical trial information: NCT03702309.

Assessment of tissue and blood tumor mutational burden in patients with melanoma using a 523-gene clinical assay.

e21570 Background: High tumor mutation burden (TMB) predicts improved efficacy of immune checkpoint inhibitors (ICIs) across a range of malignancies, including melanoma. Circulating tumor DNA (ctDNA) has emerged as a powerful complement to tumor biopsies for the diagnosis and clinical management of cancer patients. The TruSight Oncology 500 (TSO500) clinical assay interrogates 523 cancer-related genes and has shown good concordance between tissue and ctDNA using a high throughput sequencer such as NovaSeq. There are no studies looking at concordance and utility of this assay using more affordable mid throughput platforms. Here we present a pilot study comparing TSO500 sequencing results from matched tumor and plasma specimens and concordance of selected actionable gene variants investigated by ctDNA digital PCR. Methods: Samples from 18 metastatic cutaneous melanoma patients with matched formalin-fixed, paraffin-embedded (FFPE) tumor tissue and plasma collected in Streck tubes had DNA extracted for library preparation using the Illumina TSO500 NGS assay with inputs of ≥40ng of FFPE DNA and ≥10ng of ctDNA. Libraries were sequenced on a NextSeq2000 P3 flow cell to achieve recommended sequencing depth of 800 million reads per sample. A TMB cut off ≥10 mut/Mb was used as high TMB. Droplet digital PCR (ddPCR) was performed for orthogonal validation of selected clinically significant somatic mutations. Results: Sequencing on the NextSeq2000 achieved an average of 797 million pass filter reads per sample and somatic variant allele frequency (VAF) sensitivity down to 0.12%, which exceeded vendor recommendations. There was 75% concordance on the TMB classification (low and high values, Cohen’s k = 0.714) based on tumor and plasma (r = 0.86, p < 0.01) on 8 paired samples (extended analysis will be presented). Some high TMB cases carried POLE or POLD1 variants. Actionable variants identified by ctTSO500 in 15 cases were confirmed by ddPCR, with an outstanding concordance of their VAF (R2= 0.99, p < 0.0001). Diagnosis of tier I/II actionable variants (21 variants; 81% accuracy) was achieved in 7 matched tumor tissue and blood samples. Some variants found in tumor tissue were not detected in the blood. Conclusions: This pilot study demonstrates the clinical utility of the TSO500 ctDNA panel using an affordable mid throughput sequencing platform to identify actionable variants and TMB from blood specimens with high sensitivity and specificity. Testing of a larger cohort of matched tumor and plasma samples will serve to evaluate the clinical utility of the TSO500 ctDNA panel as a complement or alternative strategy to tissue biopsy for the genomic profiling of melanoma patients.

Serial postoperative ctDNA monitoring of breast cancer recurrence.

562 Background: Up to 30% of patients with breast cancer relapse after primary treatment. There are no sensitive or reliable tests to monitor these patients and detect distant metastases before overt recurrence. Here, we demonstrate the use of personalized circulating tumour DNA (ctDNA) profiling performed postoperatively, postadjuvantly, and serially for detection of recurrence in breast cancer. Methods: Patients with primary breast cancer (n=188) were recruited following surgery and adjuvant therapy and were followed-up for up to 10 years with semi-annual blood sampling for ctDNA analysis. Patients (n=29) with insufficient residual tumour for whole exome sequencing (WES) were excluded from the analysis. Tumour WES profiles were generated for 159 patients; samples from 2 patients failed WES QC requirements and a personalised ctDNA panel could not be generated for 1 patient. In 156 patients, plasma samples (n=1141) were retrospectively tested for the presence of ctDNA using personalized Signatera assays (mPCR-NGS) targeting up to 16 somatic single nucleotide variants selected from primary tumour WES. Results: Plasma ctDNA was detected ahead of clinical or radiologic relapse in 30 of the 34 relapsed patients (sensitivity of 88%). Metastatic relapse was predicted with a lead interval of up to 2 years (median: 10 months, range: 0-39 months); median lead intervals for HR+/HER2- were 15 (2 - 39); for HR-/HER2+ 6 (0.5 – 12) for HR+/HER2+ 8 (5 – 14) and 9 (0-20) for TNBC. Patients with a positive ctDNA test had poorer relapse-free-survival (RFS) (HR=47.5; 95% CI 18.5-161.4; p <0.001) from surgery and all four breast cancer subgroups showed a similarly reduced RFS. Overall survival was also significantly reduced for patients who were ctDNA positive (HR=84.15; 95%CI 16.43-1538; p <0.001). The number of variants, mean VAF and MTM/mL varied between patients, with significantly higher values at the time closest to relapse than in the first ctDNA positive sample (p =0.0002). Among the 4 relapsed patients not detected in the study all were HR+/HER2-, 1 had a local recurrence, 2 had bone recurrence (1 with axillary LN involvement) and 1 had cancer cells in pleural fluid. Of the remaining 122 patients, only 5 developed ctDNA-positivity, all with low VAF, none of them have relapsed by the follow-up census date (31 December 2021). However, follow-up for some of these patients limits definitive assessment. Lastly, 4 patients developed a second primary cancer (2 breast, 2 lung) all of whom were ctDNA-negative. Conclusions: This study demonstrates that serial post-operative ctDNA analysis has strong prognostic value. More importantly, earlier detection of metastatic disease provides a possible window for therapeutic intervention, while repeated negative ctDNA tests can provide reassurance to patients. Future interventional studies may assess the clinical utility of ctDNA-based risk-stratification.

Anchored Multiplex PCR Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA.

Detection of melanoma mutations using circulating tumor DNA (ctDNA) is a potential alternative to using genomic DNA from invasive tissue biopsies. To date, mutations in the GC-rich TERT promoter region, which is commonly mutated in melanoma, have been technically difficult to detect in ctDNA using next-generation sequencing (NGS) panels. In this study, we developed a custom melanoma NGS panel for detection of ctDNA, which encompasses the top 15 gene mutations in melanoma including the TERT promoter. We analyzed 21 stage III and IV melanoma patient samples who were treatment-naïve or on therapy. The overall detection rate of the custom panel, based on BRAF/NRAS/TERT promoter mutations, was 14/21 (67%) patient samples which included a TERT C250T mutation in one BRAF and NRAS mutation negative sample. A BRAF or NRAS mutation was detected in the ctDNA of 13/21 (62%) patients while TERT promoter mutations were detected in 10/21 (48%) patients. Co-occurrence of TERT promoter mutations with BRAF or NRAS mutations was found in 9/10 (90%) patients. The custom ctDNA panel showed a concordance of 16/21 (76%) with tissue based-detection and included 12 BRAF/NRAS mutation positive and 4 BRAF/NRAS mutation negative patients. The ctDNA mutation detection rate for stage IV was 12/16 (75%) and for stage III was 1/5 (20%). Based on BRAF, NRAS and TERT promoter mutations, the custom melanoma panel displayed a limit of detection of ~0.2% mutant allele frequency and showed significant correlation with droplet digital PCR. For one patient, a novel MAP2K1 H119Y mutation was detected in an NRAS/BRAF/TERT promoter mutation negative background. To increase the detection rate to >90% for stage IV melanoma patients, we plan to expand our custom panel to 50 genes. This study represents one of the first to successfully detect TERT promoter mutations in ctDNA from cutaneous melanoma patients using a targeted NGS panel.

Abstract P5-13-29: Analytical and clinical validation of a ctDNA assay for detecting copy number loss and structural rearrangement variants contributing to homologous recombination and repair (HRR) deficiency

Abstract Background: Inactivating HRR gene mutations can lead to HRR deficiency (HRD) and predict response to PARPi therapy in patients with breast cancer. Copy number loss and large genomic rearrangements (LGR) can result in HRD but are challenging to detect in ctDNA. Here, we present the analytical validation of homozygous deletions, loss of heterozygosity (LoH) and LGR detection on the Guardant360 (G360) liquid biopsy panel, previously validated for detection of small variants, copy number amplifications, and fusions. We present real-world outcomes of BRCA1/2-mutant PARPi-treated patients to demonstrate the clinical validity of the detected variants. Methods: Analytical validation was performed using the G360 83-gene ctDNA panel. Cell line DNA and clinical patient cfDNA were titrated into matched normal cell line DNA or healthy donor cfDNA to establish the limit of detection (LoD) and precision for copy number loss and LGRs, respectively. Accuracy results were compared to those from an orthogonal, externally validated tissue and ctDNA panel. De-identified, longitudinal, claims data were linked to the cancer genomic profiles in Guardant INFORM, a clinical-genomics database. Advanced PARPi treated breast cancer patients with an inactivating or reversion BRCA1/2 mutation detected by G360 were assessed. Results: The analytical sensitivity (95% LoD) for detecting homozygous and LoH deletions for deletion sizes >10MB was established at tumor fractions (TF) of 12.5% and 25%, respectively. The 95% LoD for LGRs was 0.2% variant allele fraction (VAF). The per-sample false positive rate for copy number loss and LGRs was <0.5%. Prevalence of BRCA1/2 homozygous deletions, LoH and LGRs in >1000 advanced breast cancer patients was 1.8%, 16.6% and 0.25% respectively, compared to 2.4%, 56.7% and 0.3% in TCGA. To verify the clinical impact of cfDNA-detected HRR alterations, overall survival was determined for PARPi-treated patients with >1 BRCA1/2 germline or somatic SNV, indel or LGR reversion mutation to be 23.2 months [16.4, 30, CI, n=75] compared to 54.4 [28, NA, CI, n=14] months for BRCA1/2-mutant patients without a reversion (p-value=0.049). Conclusion:. This analytical validation demonstrates that G360 detection of inactivating mutations, including copy number loss and LGRs, is highly sensitive, reliable and robust. Real-world evidence analysis confirmed worse survival outcomes in PARPi treated patients harboring a BRCA1/2 reversion compared to BRCA1/2-mutant patients with no reversion. This data further supports ctDNA as a compelling non-invasive means to identify potential PARPi sensitizing and resistance mutations in patients with advanced breast cancer. Citation Format: Jennifer Yen, Leylah Drusbosky, Caroline Weipert, Nicole Zhang, David Hanna, Catalin Barbacioru, Hao Wang, Alex Artyomenko, Arielle Yablonovitch, Yu Fu, Aaron Hardin, Nagesh Alla, Robert Foley, Max Maligska, Bhargavi Panchangam, Phil Yen, Jane Meisel, Neelima Vidula, Massimo Cristofanilli, Jeremy Force, Michael Dorschner, Martina Lefterova, Elena Helman, Becky Nagy, Darya Chudova, AmirAli Talasaz. Analytical and clinical validation of a ctDNA assay for detecting copy number loss and structural rearrangement variants contributing to homologous recombination and repair (HRR) deficiency [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-29.

P21.01 Selected ctDNA Panel Gene Sequencing for Neoantigen Discovery and Survival Prediction in Patients With Stage IV Non-Small Cell Lung Cancer

Tumor neoantigens are ideal targets for immunotherapy with current work largely limited on the whole-exome sequencing data from tumor tissues which are often limited by tissue availability. The ctDNA is now widely used for genomic testing of selected panel genes but has not been tested for neoantigen assessment. The purposes of this study were to study 1) whether is it possible to discover tumor neoantigens through panel gene sequencing of ctDNA, and 2) whether the tumor neoantigens of ctDNA has significance on the prognosis.

5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC.

148 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of metastatic castration-resistant prostate cancer (mCRPC) and to evaluate the potential of 5hmC modifications in cfDNA as biomarkers of outcome in mCRPC patients. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in DNA from 93 mCRPC tissue biopsies previously profiled with whole-genome sequencing (WGS), RNA-sequencing and whole-genome bisulfite sequencing (WGBS). In addition, we analyzed 64 cell-free DNA (cfDNA) samples, from men with mCRPC before first-line abiraterone or enzalutamide, with both 5hmC sequencing and a conventional targeted ctDNA panel assessing common genomic alterations. Results: In mCRPC tissue samples, 5hmC enrichment was more strongly associated with gene expression than promoter methylation or copy number. Among cancer hallmark pathways, the androgen response genes had the strongest association between 5hmC and gene expression, suggesting a disease specific marking of gene activation. 5hmC patterns in cfDNA could be used to estimate the circulating tumor DNA fraction (ct-fraction), which was prognostic for overall survival (tertiles of ct-fraction, HR = 1.6 95%CI 1.1-2.3, p = 0.007). Further, 5hmC levels were indicative of gain of oncogene activity (such as AR, MYC, and PIK3CA) and loss of tumor suppressor gene activity (such as RB1, TP53 and BRCA2). The number of alterations, by 5hmC levels, of common drivers of mCRPC was prognostic for overall survival, also after adjusting for ct-fraction (adjusted p = 0.00001), and the prognostic value of common alterations detected by 5hmC sequencing versus conventional targeted ctDNA sequencing was similar. Finally, 5hmC levels in cfDNA of genes not significantly altered by copy number gain or loss (and thus not routinely included in targeted ctDNA sequencing assays), such as TOP2A and EZH2, identified a high-risk subgroup of mCRPC, which was highly prognostic for overall survival independent of ct-fraction (adjusted HR = 1.8 95%CI 1.2-2.8, p = 0.007). Conclusions: 5hmC in mCRPC tissue demonstrated an association with gene expression that was highest for prostate cancer driver genes, highlighting the ability to track disease-specific biology. 5hmC in cfDNA from men with mCRPC can be used to estimate the ct-fraction of the sample, infer activity gain and loss of common drivers of mCRPC, and identify high-risk groups of mCRPC based on alterations not commonly detected with conventional ctDNA sequencing, showing its potential as a liquid biomarker. Further studies are aimed at optimizing and validating 5hmC-based biomarkers in larger cohorts.

Abstract PD2-06: Clinical outcomes of alpelisib plus fulvestrant in hormone receptor-positive, human epidermal growth factor receptor-2-negative advanced breast cancer with PIK3CA alterations detected in plasma ctDNA by next-generation sequencing: Biomarker analysis from the SOLAR-1 study

Abstract Introduction: The PI3K pathway is often hyperactivated in cancer as a result of an altered PI3K isoform and/or loss of phosphatase and tensin homolog function. Approximately 40% of patients (pts) with hormone receptor-positive (HR+), human epidermal growth factor receptor-2-negative (HER2−) advanced breast cancer (ABC) have tumors with mutations in PIK3CA, which encodes the α-isoform of PI3K, p110α. These mutations are known to cause hyperactivation of the PI3K pathway, which contributes to cell proliferation, drug resistance, and poor prognoses. Alpelisib (ALP) is an α-selective PI3K inhibitor that, in combination with fulvestrant (FUL), prolonged median progression-free survival (mPFS) in pts with HR+, HER2−, PIK3CA-mutant ABC following progression on/after prior aromatase inhibitor in the phase 3 SOLAR-1 trial. In SOLAR-1, prospective PIK3CA mutation testing was performed on tumor tissue using PCR-based assays. Through retrospective analysis, efficacy of ALP was demonstrated in subgroups of pts with PIK3CA alteration(s) in tumor tissue and mutation(s) in ctDNA, detected by next-generation sequencing (NGS) and PCR, respectively. In this exploratory biomarker analysis, we assessed clinical outcomes of pts with PIK3CA alteration(s), detected in ctDNA by NGS.Methods: SOLAR-1 is a phase 3, randomized, double-blind, placebo-controlled study of ALP 300 mg vs placebo taken daily with FUL 500 mg every 28 days + Cycle 1 Day 15 in men and postmenopausal women with HR+, HER2- ABC. Retrospectively, the full exonic region of the PIK3CA gene was sequenced using the Foundation Medicine 324-gene ctDNA panel in plasma ctDNA collected at baseline. mPFS was assessed using Kaplan-Meier methodology per investigator assessment.Results: Of 572 pts in SOLAR-1, 381 pts (66.6%) across both PIK3CA-mutant and nonmutant cohorts had valid plasma ctDNA data. Of these pts, 193 (50.7%) had a PIK3CA alteration; 168 (87%) had PCR-detectable mutations and 147 (76%) had a single alteration. A total of 70 (36%) and 102 (53%) pts had alterations in exons 9 and 20, respectively. ALP plus FUL prolonged mPFS in pts with PIK3CA alterations detected in plasma ctDNA by NGS (n=101; Table). Clinical benefit was also observed in pts with PCR-detectable mutations (n=88), single mutations (n=83), and pts with mutations in exon 9 (n=34) and exon 20 (n=54). Pt numbers were low, and wide 95% CIs were observed in groups with alterations not detectable by PCR (n=13) and in pts with multiple alterations. Some limitations of this retrospective plasma analysis include that this is a subgroup (66.6%) of the SOLAR-1 pt population and that the subgroup of pts with non-altered PIK3CA included pts with a PIK3CA mutation in their tumor tissue. Conclusions: ALP plus FUL demonstrated clinical benefit in pts with PIK3CA mutations detected in plasma ctDNA by NGS, in pts with single alterations, and in pts with alterations in exons 9 and 20. Results were consistent across pt groups, except in those with alterations not detectable by PCR. In conclusion, these data demonstrate a consistent clinical benefit of ALP plus FUL in various groups of pts with PIK3CA alterations detected in ctDNA by NGS. Clinical Outcomes of Patients With PIK3CA Alterations Detected in Plasma ctDNA by NGS in SOLAR-1Alpelisib + fulvestrantPlacebo + fulvestrantHR (95% CI)Events/N (%)mPFS, mo (95% CI)Events/N(%)mPFS, mo (95% CI)PIK3CA altered vs non-alteredAltered58/101(57.4)11.04(7.72-16.16)73/92(79.3)3.65(2.86-6.80)0.47(0.33-0.67)Non-altered40/87(46.0)10.87(5.59-16.76)60/101(59.4)5.45(3.75-9.00)0.60(0.40-0.91)PIK3CA: alteration detectable by PCR vs alteration not detectable by PCRDetectable52/88(59.1)12.48(7.36-18.37)66/80(82.5)3.58(2.37-5.65)0.44(0.30-0.64)Not detectable6/13(46.2)8.48(2.69-NA)7/12(58.3)7.39(1.87-12.98)1.12(0.35-3.56)PIK3CA: number of alterationsSingle45/83(54.2)12.88(7.36-18.50)50/64(78.1)3.58(1.87-6.11)0.43(0.28-0.65)Multiple13/18(72.2)9.00(3.68-18.37)23/28(82.1)4.63(3.48-9.63)0.55(0.25-1.20)PIK3CA alterations in exon 9 or exon 20Exon 918/34(52.9)15.21(7.03-NA)29/36(80.6)3.66(2.86-7.36)0.31(0.16-0.61)Exon 2034/54(63.0)10.91(5.72-18.37)40/48(83.3)3.52(1.87-6.11)0.51(0.31-0.82)CI, confidence interval; ctDNA, circulating tumor DNA; HR, hazard ratio; mPFS, median progression-free survival; mo, months; NA, not available; NGS, next-generation sequencing. Citation Format: Eva M. Ciruelos, Sibylle Loibl, Ingrid A. Mayer, Mario Campone, Hope S. Rugo, Monica Arnedos, Hiroji Iwata, Pier Franco Conte, Fabrice André, Albert Reising, Chong Ma, Michelle Miller, Naveen Babbar, Dejan Juric. Clinical outcomes of alpelisib plus fulvestrant in hormone receptor-positive, human epidermal growth factor receptor-2-negative advanced breast cancer with PIK3CA alterations detected in plasma ctDNA by next-generation sequencing: Biomarker analysis from the SOLAR-1 study [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD2-06.

Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling

The incidence of esophageal adenocarcinoma (EAC) is rapidly rising and has a 5-year survival rate of <20%. Beyond TNM (tumor-node-metastasis) staging, no reliable risk stratification tools exist and no large-scale studies have profiled circulating tumor DNA (ctDNA) at relapse in EAC. Here we analyze the prognostic potential of ctDNA dynamics in EAC, taking into account clonal hematopoiesis with indeterminate potential (CHIP). A total of 245 samples from 97 patients treated with neoadjuvant chemotherapy and surgery were identified from the prospective national UK Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium data set. A pan-cancer ctDNA panel comprising 77 genes was used. Plasma and peripheral blood cell samples were sequenced to a mean depth of 7082× (range 2196-28524) and ctDNA results correlated with survival. Characteristics of the 97 patients identified were as follows: 83/97 (86%) male, median age 68 years (SD 9.5 years), 100% cT3/T4, 75% cN+. EAC-specific drivers had higher variant allele fractions than passenger mutations. Using stringent quality criteria 16/79 (20%) were ctDNA positive following resection; recurrence was observed in 12/16 (75%) of these. As much as 78/97 (80%) had CHIP analyses that enabled filtering for CHIP variants, which were found in 18/78 (23%) of cases. When CHIP was excluded, 10/63 (16%) patients were ctDNA positive and 9/10 of these (90%) recurred. With correction for CHIP, median cancer-specific survival for ctDNA-positive patients was 10.0 months versus 29.9 months for ctDNA-negative patients (hazard ratio 5.55, 95% confidence interval 2.42-12.71; P= 0.0003). Similar outcomes were observed for disease-free survival. We demonstrate in a large, national, prospectively collected data set that ctDNA in plasma following surgery for EAC is prognostic for relapse. Inclusion of peripheral blood cell samples can reduce or eliminate false positives from CHIP. In future, post-operative ctDNA could be used to risk stratify patients into high- and low-risk groups for intensification or de-escalation of adjuvant chemotherapy.

Abstract 1974: Clonal and subclonal mutational landscapes in circulating tumor DNA in metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study

Abstract Introduction: We performed an exploratory analysis of circulating tumor DNA (ctDNA) in patients (pts) with RAS wild-type (WT) chemotherapy-naïve stage IV metastatic colorectal cancer (mCRC) from the ongoing phase III PARADIGM study (NCT02394834). The clonal and subclonal mutational landscapes of RAS WT pts were analyzed using a mCRC-focused custom ctDNA sequencing panel. Methods: Randomized pts (1:1) received mFOLFOX6 plus either panitumumab or bevacizumab. Pre-treatment plasma samples (DNA yield &amp;gt;10ng/mL and &amp;gt;10nM) were sequenced using the custom ctDNA panel (PlasmaSELECTTM-R 91, PGDx) to detect mCRC mutations, amplifications, and rearrangements in 90, 26, and 3 genes, respectively, as well as microsatellite instability (MSI), in 250kb targeted regions using stringent quality criteria. Pre-treatment archival tissue samples from 590 pts were analyzed by the Broad Institute Solid Tumor panel, which covered 1,072 genes with 7.3Mb targeted regions. Results: Between May 29, 2015 and June 8, 2017, 823 pts were enrolled across 197 sites. Plasma samples were collected from 756 pts, with 747 (98.8%) samples meeting the quality criteria. The average total and distinct sequencing coverages were 34,200 and 5,865, respectively, with 49.1% of bases mapping to regions of interest. Mutation frequencies in ctDNA were generally consistent with those observed in RAS-WT TCGA CRC and rectal cancers (n=283), except for TET2 and DNMT3A potentially due to clonal hematopoiesis. Mutations in BRAF, APC, CTNNB1, PTEN, PIK3CA, and MSI-status observed in ctDNA were significantly different between left and right-sided tumors, consistent with known differences in tumor sidedness. In the 747 plasma samples, 4,072 mutations were observed; 1,871 had a mutant allele frequency (MAF) &amp;lt;25% of the highest MAF in each sample (defined as subclonal) and 2,201 had a MAF above this threshold (defined as clonal). Clonal mutations were 77.5% concordant with mutations in corresponding tissue samples. Subclonal mutations showed 17.3% concordance between tissue and plasma, suggesting that tumor heterogeneity may result in subclonal mutations in ctDNA. Although pts with KRAS/NRAS mutations (G12, G13, A59, Q61, K117, A146) in archival FFPE tissue were not eligible for this study, 38 RAS mutations (58% subclonal) were observed in ctDNA of 32 pts, suggesting that sub-populations of tumor cells may have KRAS mutations in these cases. Patient-level subclonality analyses suggested that the fraction of subclonal mutations were higher in pts with metastases in ≥2 organ sites. Conclusion: The validated ultra-deep plasma sequencing panel was concordant with tissue sequencing and detected tumor heterogeneity. The PARADIGM study will report the efficacy of anti-EGFR/VEGF therapies; post-treatment collection of ctDNA is ongoing. The relationship between therapeutic effects and clonal and subclonal mutational landscapes will be examined in the future. Funded by Takeda Pharmaceutical Company Limited, Tokyo, Japan. ClinicalTrial.gov number: NCT02394834 Citation Format: Katsuya Tsuchihara, Riu Yamashita, Takayuki Yoshino, Kohei Shitara, Jun Watanabe, Hirofumi Yasui, Hisatsugu Ohori, Manabu Shiozawa, Kentaro Yamazaki, Eiji Oki, Takeo Sato, Takeshi Naitoh, Yoshito Komatsu, Takeshi Kato, Kazunori Yamanaka, Ikuo Mori, Masamitsu Hihara, Junpei Soeda, Takeharu Yamanaka, Kiwamu Akagi, Atsushi Ochiai, Kei Muro, Victor E. Velculescu, Hiroyuki Uetake. Clonal and subclonal mutational landscapes in circulating tumor DNA in metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1974.

A basket trial of trastuzumab deruxtecan, a HER2-targeted antibody-drug conjugate, for HER2-amplified solid tumors identified by circulating tumor DNA analysis (HERALD trial).

TPS3650 Background: Trastuzumab deruxtecan, a new HER2-targeting antibody-drug conjugate, has been approved for unresectable or metastatic HER2-positive breast cancer by the Food and Drug Administration. In a phase I/II trial, trastuzumab deruxtecan showed a manageable safety profile and antitumor activity in HER2-positive various cancer types. In addition, a tissue-based HER2 test occasionally cannot identify accurate HER2 status due to spatial and temporal intratumoral heterogeneity, leading to potentially missing an opportunity for responders to receive benefit from anti-HER2-targeted therapy. Circulating tumor DNA (ctDNA) analysis can detect comprehensive somatic genome alterations by assessment of spatial and temporal intratumoral heterogeneity with minimal invasiveness. Methods: We designed an investigator-initiated multicenter phase II basket trial to evaluate efficacy and safety of trastuzumab deruxtecan in advanced solid tumor malignancies with HER2 amplification identified by Guardant360, a 74-gene sequencing ctDNA panel, as a part of the Nationwide Cancer Genome Screening Project (GOZILA study, UMIN000029315). The key eligibility criteria are as follows: 1) Histopathologically confirmed advanced solid tumor malignancy; 2) Identified HER2 amplification by Guardant360; 3) Failed prior standard therapy. The participants will receive intravenously 5.4 mg/kg of trastuzumab deruxtecan every 3 weeks. The primary endpoint is objective response rate (ORR). The planned sample size is 55-65. A Bayesian model considering the potential heterogeneity across cancer types will be applied to detect ORR of 5% versus 25% to a certain level while maintaining the false-positive error rate in each cancer type at 10%. Furthermore, tumor tissue, ctDNA and circulating tumor cells are serially collected and analyzed to investigate the predictive biomarkers and resistance mechanisms. The trial was activated in late 2019. At the time of the abstract submission, 2 patients have been enrolled. This trial is granted by AMED under Grant Number JP18lk0201084. Clinical trial information: JapicCTI-194707 .

Genomic landscape of circulating tumor (ct)-DNA alterations in patients with penile cancer.

6 Background: Penile cancer is a rare disease associated with HPV infection and harbors recurrent somatic genomic alterations in the ERBB (HER)-family, CDKN2A, TP53, NOTCH1 and PIK3CA. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution. To our knowledge, the genomic alterations observed in ctDNA for penile cancer have not been described before. We report ctDNA profiling of patients with advanced penile cancer. Methods: Sixteen pts with metastatic penile cancer from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Three patients had at least one serial ctDNA sample. De-identified demographic data were collected. Guardant 360 is CLIA-certified ctDNA panel that assesses single nucleotide variants and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants seen at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or reported in OncoKB were considered pathogenic. Results: The median age was 64 years (range 40-77). 4 pts (25%) were documented to be post platinum-based chemotherapy. Among the entire cohort, 51 ctDNA alterations were detected (median=2, range 0-6) in 15/16 patients (94%) across 21 genes (table). Of the 51 alterations, 24 (47%) were actionable and had approved targeted therapies in other cancers. Alterations were most frequently detected in TP53 (9/16, 56%), CDKN2A (5/16, 31%), and TERT promoter (5/16, 31%) (table). In 3 patients with serial samples, 9 novel pathogenic alterations were detected in the second sample including ATM, CDKN2A, ARID1A, CCND1, CDK6, EGFR, PDGFRA, PIK3CA, and SMAD4. Conclusions: ctDNA alterations in patients with advanced penile cancer were frequently detected and appeared similar to previously described tumor tissue analyses. New alterations found on serial ctDNA assays shed light on patterns of tumor evolution and may inform drug development for this challenging orphan malignancy.[Table: see text]

Circulating tumor (ct)-DNA alterations in patients with testicular germ cell tumors.

415 Background: Testicular germ cell tumors (GCT) infrequently harbor somatic mutations. ctDNA assessment allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. We report ctDNA profiling of patients (pts) with testicular GCTs. Methods: 40 patients (pts) with advanced testicular GCTs from multiple institutions in the USA that underwent ctDNA analysis using the Guardant (G)-360 platform were eligible and a total of 48 samples were collected. 36 pts had one sample, 3 pts had 2 samples, 1 pt had 6 samples. De-identified demographic data were collected in addition to data for ctDNA alterations. G360 employed a CLIA-certified ctDNA panel that assessed single nucleotide variant and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants reported at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or found in OncoKB were considered pathogenic. Results: Of 40 patients with testicular GCTs, 13pts (33%) were post systemic therapy. The median age was 36 years (range 20-61). 199 ctDNA alterations were detected in 35 patients (87.5%) across 41 genes. Among the 199 alterations, 102 were believed to be pathogenic and detectable in 26 samples from 25 pts (62.5) (%). The most common pathogenic somatic alterations were KRAS (n = 16/102, 16%), TP53 (n = 16/102, 16%), CCND2 (n = 9/102, 9%), CDK6 (n = 9/102, 9%), MET (n = 9/102, 9%), and RAF1 (n = 6/102, 6%). Conclusions: ctDNA alterations were frequently detected in resistant testicular GCTs and appear similar to alterations previously described in tumor tissue analyses of testicular GCTs. Given that ctDNA offers a non-invasive means of profiling tumor DNA, further development of this promising modality is warranted to study the evolution of resistance to cisplatin-based chemotherapy and new potentially actionable alterations.

Association of a novel circulating tumor DNA next-generating sequencing platform with circulating tumor cells (CTCs) and CTC clusters in metastatic breast cancer

PurposeLiquid biopsies, including circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), can be used to understand disease prognosis, tumor heterogeneity, and dynamic response to treatment in metastatic breast cancer (MBC). We explored a novel, 180-gene ctDNA panel and the association of this platform with CTCs and CTC clusters.MethodsA total of 40 samples from 22 patients with MBC were included in the study. For the primary analysis, all patients had ctDNA sequencing using the PredicinePLUS™ platform. CTCs and CTC clusters were examined using the CellSearch™ System. Clinical and pathological variables were reported using descriptive analyses. Associations between CTC count and specific genomic alterations were tested using the Mann-Whitney U test.ResultsOf 43 sequenced patients, 40 (93%) had at least one detectable genomic alteration with a median of 6 (range 1–22). Fifty-seven different genes were altered, and the landscape of genomic alterations was representative of MBC, including the commonly encountered alterations TP53, PTEN, PIK3CA, ATM, BRCA1, CCND1, ESR1, and MYC. In patients with predominantly hormone-receptor-positive MBC, the number of CTCs was significantly associated with alterations in ESR1 (P < 0.005), GATA3 (P < 0.05), CDH1 (P < 0.0005), and CCND1 (P < 0.05) (Mann-Whitney U test). Thirty-six percent of patients had CTC clusters, which were associated with alterations in CDH1, CCND1, and BRCA1 (all P < 0.05, Mann-Whitney U test). In an independent validation cohort, CTC enumeration confirmed significant associations with ESR1 and GATA3, while CTC clusters were significantly associated with CDH1.ConclusionsWe report on a novel ctDNA platform that detected genomic alterations in the vast majority of tested patients, further indicating potential clinical utility for capturing disease heterogeneity and for disease monitoring. Detection of CTCs and CTC clusters was associated with particular genomic profiles.

Abstract LB-233: Analysis of personalised circulating tumour DNA to monitor recurrence and metastasis in multiple cancer types

Abstract Purpose: The evaluation of circulating tumour DNA (ctDNA) is a promising tool to monitor tumour progression and guide personalised treatments. We evaluated ctDNA in plasma samples from 521 Chinese patients with more than 12 tumour types and explored ctDNA’s ability to predict tumour status, especially recurrence and metastasis. Methods: We established a personalised ctDNA panel sequencing, which targeted trunk clonal somatic mutations of each patient calculated by CSMT-tools (monitors tumour load tools based on paired whole exon and cell-free DNA next generation sequencing data, PCT/CN2016/106284) and drug-resistant mutations. The ctDNA content fraction of all somatic mutations was then evaluated. Furthermore, 209 patients were followed up for ctDNA detection and routine examination. Results: Whole exome sequencing was performed on 1121 patients, and 97% of patients were successfully designed personalised ctDNA assays using CSMT-tools. Currently, 521 Chinese patients mainly with colorectal, liver, lung, gastric cancer, glioma or cholangiocarcinoma received at least one ctDNA detection. 66.79%, 50.86%, 42.99%, and 25.72% of these patients had detectable ctDNA with ctDNA content fractions above 0.25%, 0.5%, 1%, and 5%, respectively. At ctDNA content fraction above 0.25%, the detection rate of ctDNA in major cancer types, excluding liver, pancreatic cancer and glioma, was higher than 70%. In glioma, the rate of ctDNA detection in blood was much lower than in cerebrospinal fluid (24.29% vs 80%). Moreover, dynamic changes of ctDNA were significantly correlated with clinical outcomes for patients, with a consistency rate of 89.51%. The consistency rate of most major cancer types was above 90%, but that of glioma (71.43%) and pancreatic cancer (60%) were lower. ctDNA content fraction increased in all patients with recurrence and metastasis, from 2.72 to 59.8 fold. We also detected a drug-resistance process in a lung cancer patient with EGFR_p.E746_A750del. EGFR_p.T790M was first detected after the patient was administered gefitinib for more than a year, 3 months earlier than radiologic progression. Conclusions: Our personalised ctDNA analysis can effectively detect ctDNA. Hence, it can predict tumour progression and guide precise treatment. Citation Format: Guan Wang, Jinwang Wei, Angela Wu, Chun Dai, Wending Sun, Xin Cai, Qiang Xu. Analysis of personalised circulating tumour DNA to monitor recurrence and metastasis in multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-233.

Abstract 435: Cell-free circulating tumor DNA (ctDNA) detects somatic copy number loss in homologous recombination repair genes

Abstract Background: In addition to BRCA1/2 germline and somatic inactivating mutations, loss of heterozygosity (LOH) and biallellic somatic copy number loss are associated with BRCA1/2 loss of function. Patients with cancers harboring these somatic features may benefit from treatment with PARP inhibitors. ctDNA analysis has proven a viable alternative to tumor tissue genotyping, especially in tissue- or time-limited clinical scenarios. However, ctDNA assessment of LOH and biallelic copy number loss is challenging given that ctDNA is diluted by cell-free leukocytic DNA making it difficult to confidently call these genomic events. We developed a method to identify somatic biallelic copy number loss in ctDNA using targeted sequencing of cell-free (cfDNA) across a wide range of cancer types. Methods: A novel statistical model was developed using coverage profiles and single nucleotide polymorphism (SNP) allelic frequencies estimated from plasma samples to determine the presence of LOH and biallellic copy number loss in BRCA1 or BRCA2. For each gene of interest, the model uses observed coverage and fragment size distribution, together with allele frequency of germline SNPs. The model was applied to plasma samples from 28,000 patients with advanced solid tumors sequenced using a 73-gene next generation sequencing ctDNA panel (Guardant360®, Guardant Health, Redwood City, CA). Results: The model was analytically validated using in-silico simulations in order to assess both the limit of blank and limit of detection. This method shows 95% sensitivity in detecting LOH and bi-allellic copy number loss for samples with a maximum somatic variant allele frequency as low as 9%. Sensitivity is mainly driven by the panel size and the depth of coverage of the gene of interest. The model was then applied to the 28,199 patient cohort. BRCA1 and BRCA2 LOH was observed in 2.4% (134/5568) and 7.4% (415/5568) of classic homologous recombination deficient (HRD) cancers including breast, ovarian, prostate, and pancreas. BRCA1 and BRCA2biallelic copy number loss was observed in 0.3% (19/5568) and 0.6% (31/5568) of this same group of HRD cancers. Discussion: In this cohort of 5,568 patients with classic HRD associated cancers, somatic LOH and biallelic copy number loss was detected in BRCA1 in 2.7% of samples and in BRCA2 in 8.0% of samples, which is aligned with previously reported tissue prevalence. BRCA1/2 somatic LOH and biallelic copy number loss can accurately be detected in ctDNA utilizing likelihood-based scores based on coverage and germline SNPs allele frequencies. The ability to identify this therapeutically targetable genomic alteration through a non-invasive ctDNA assessment has significant clinical implications. Citation Format: Catalin Barbacioru, Victoria M. Raymond, Marcin Sikora, Elena Helman, Sante Gnerre, Stephen Fairclough, Darya Chudova, Richard B. Lanman, AmirAli Talasaz. Cell-free circulating tumor DNA (ctDNA) detects somatic copy number loss in homologous recombination repair genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 435.

TiFFANY study: A multicenter phase II basket-type clinical trial to evaluate efficacy and safety of pan-FGFR inhibitor TAS-120 for advanced solid malignancies with FGFR alterations identified by circulating tumor DNA.

TPS3156 Background: Approximately 7% of advanced solid malignancies have FGFR gene alterations. However, standard treatment for FGFR-altered malignancies has not been established. Moreover, circulating tumor DNA (ctDNA) analysis has a potential to accurately identify FGFR alterations by assessing spatial and temporal intratumoral heterogeneity, which have shown to be associated with a poor prognosis and resistance to anti-cancer therapy. Methods: We are conducting an investigator-initiated multicenter phase II basket-type trial to investigate efficacy and safety of TAS-120, a highly selective covalent pan-FGFR inhibitor, for the patients with advanced solid malignancies with FGFR alterations identified by ctDNA analysis as a part of the Nationwide Cancer Genome Screening Project (GOZILA study, UMIN000029315). Eligibility criteria include histologically confirmed unresectable advanced or recurrent solid tumors regardless of histology of origin; ECOG PS of 0 or 1; refractory or intolerant to the standard therapies; and clonal FGFR alterations ( FGFR1-3 gain-of-function mutations, FGFR1,2 amplifications and FGFR2,3 fusions) identified by a 73-gene sequencing ctDNA panel (Guardant360). Enrolled patients will receive TAS-120 20 mg once daily, orally, in a 21 day-cycle. The primary endpoint is to clarify objective response rate (ORR) assessed by investigators per RECIST v1.1. The secondary endpoints are to evaluate progression-free survival, duration of response, time to treatment failure, disease control rate, overall survival, ORR by central determination, and incidence of adverse events. Target sample size is determined as 26 to test the null hypothesis of ORR as 5% with one-sided alpha level of 2.5% and power of 80% to detect an expected value of ORR as 25%. Furthermore, tumor tissue and ctDNA will be serially collected and analyzed to investigate the resistance mechanisms and provide clinically meaningful biomarker which may be used for identifying and implementing treatment changes. Clinical trial information: 194624.

Circulating tumor (ct)-DNA alterations in patients with testicular germ tumors.

e16063 Background: Testicular germ cell tumors (GCT) infrequently harbor somatic mutations. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. To our knowledge, ctDNA genomic alterations observed in in testicular GCTs have not been heretofore described. We report ctDNA profiling of patients (pts) with testicular GCTs. Methods: 31 Pts with testicular GCTs from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Two patients had one serial ctDNA sample. De-identified demographic data were collected in addition to data for ctDNA alterations. Guardant360 is a CLIA-certified ctDNA panel that assesses single nucleotide variant and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants reported at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or found in OncoKB were considered pathogenic. Results: Of 31 patients with testicular GCTs, 162 ctDNA alterations were detected in 26 patients (84%) across 41 genes (Table). A median number of 3 alterations (range 1-19) was detected per sample. Among the 162 alterations, 88 were believed to be pathogenic and detectable in 20 patients (65%). 12/31 pts (39%) were documented to be post systemic therapy. The median age was 38 years (range 20-61). The most common pathogenic somatic alterations were KRAS (n = 12/88, 14%), CCND2 (n = 8/88, 9%), MET (n = 8/88, 9%), CDK6 (n = 7/88, 8%), TP53 (n = 6/88, 7%), and RAF1 (n = 5/88, 6%). In 2 patients with serial samples, 5 novel pathogenic alterations were detected in the second sample including FGFR2, APC, CDK6, RAF1, and MAPK1. Conclusions: ctDNA alterations were frequently detected in resistant testicular GCTs and appear similar to alterations previously described in tumor tissue analyses of testicular GCTs. Given that ctDNA offers a non-invasive means of profiling tumor DNA, further development of this promising modality is warranted to determine it's relevance in clinical practice. [Table: see text]

Genomic landscape of circulating tumor (ct)-DNA alterations in patients with penile cancer.

e16027 Background: Penile cancer is a rare disease associated with HPV infection and is known to harbor recurrent somatic genomic alterations in the ERBB (HER)-family, CDKN2A, TP53, NOTCH1 and PIK3CA. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. To our knowledge, the genomic alterations observed in ctDNA for penile cancer have not been described before. We report ctDNA profiling of patients with advanced penile cancer. Methods: Sixteen pts with metastatic penile cancer from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Three patients had at least one serial ctDNA sample. De-identified demographic data were collected. Guardant 360 is CLIA-certified ctDNA panel that assesses single nucleotide variants and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants seen at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or reported in OncoKB were considered pathogenic. Results: The median age was 64 years (range 40-77). 4 pts (25%) were documented to be post platinum-based chemotherapy. The median number of ctDNA alterations detected per sample was 2 (range 0-6). Overall, genomic alterations were detected in 15/16 patients (94%) across 21 genes (table 1). Alterations were most frequently detected in TP53 (9/16, 56%), CDKN2A (5/16, 31%), TERT promoter (5/16, 31%), PIK3CA (3/16, 19%) and ERBB2 (3/16, 19%). In 3 patients with serial samples, 9 novel pathogenic alterations were detected in the second sample including ATM, CDKN2A, ARID1A, CCND1, CDK6, EGFR, PDGFRA, PIK3CA, and SMAD4. Conclusions: ctDNA alterations in patients with advanced penile cancer were frequently detected with similar prevalences to previously described tumor tissue analyses. New alterations observed on serial ctDNA assays may provide insights regarding tumor biology and inform drug development. [Table: see text]